13-99429512-C-T

Variant names:

• chr13-99429512-C-T
• rs9585056
• ENST00000646895.1:n.887G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646895.1(LNCARGI):​n.887G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,008 control chromosomes in the GnomAD database, including 38,765 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.71 (38765 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LNCARGI ENST00000646895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 35 publications found

Genes affected

LNCARGI (HGNC:56890):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCARGI	NR_197584.1	n.935G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LNCARGI	NR_197585.1	n.781G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LNCARGI	NR_197586.1	n.1122G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCARGI	ENST00000646895.1	n.887G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107855 AN: 151890 Hom.: 38747 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.724

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.710 AC: 107918 AN: 152008 Hom.: 38765 Cov.: 32 AF XY: 0.711 AC XY: 52838 AN XY: 74304

African (AFR) AF: 0.597 AC: 24715 AN: 41404

American (AMR) AF: 0.707 AC: 10807 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3470

East Asian (EAS) AF: 0.934 AC: 4834 AN: 5176

South Asian (SAS) AF: 0.685 AC: 3300 AN: 4816

European-Finnish (FIN) AF: 0.759 AC: 8017 AN: 10562

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51216 AN: 67978

Other (OTH) AF: 0.724 AC: 1527 AN: 2108

Alfa AF: 0.738 Hom.: 57382

Bravo AF: 0.706

Asia WGS AF: 0.770 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.73
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9585056; hg19: chr13-100081766;